Add the 'xtalsymm' action

README.md

@@ -45,7 +45,7 @@ CPPTRAJ see the following publication:
 Disclaimer and Copyright
 ========================
 
-CPPTRAJ is Copyright (c) 2010-2018 Daniel R. Roe.
+CPPTRAJ is Copyright (c) 2010-2019 Daniel R. Roe.
 The terms for using, copying, modifying, and distributing CPPTRAJ are 
 specified in the file LICENSE.
 
@@ -165,6 +165,9 @@ Code for the reciprocal part of the particle mesh Ewald calculation.
 * Christina Bergonzo (National Institute of Standards and Technology, Gaithersburg, MD)  
 Fixes and improvements to nucleic acid dihedral angle definitions (DihedralSearch).
 
+* David S. Cerutti (Rutgers University, Piscataway, NJ, USA)  
+Original code for the 'xtalsymm' Action.
+
 #### Various Contributions
 * David A. Case (Rutgers University, Piscataway, NJ, USA)
 * Hai Nguyen (Rutgers University, Piscataway, NJ, USA)

configure

@@ -130,9 +130,6 @@ USE_CPPTRAJDEBUG=0   # Enable internal cpptraj debug flags
 CLEAN='yes'          # yes = clean after configure, no = do not
 PERFORM_CHECKS='yes' # yes = Check compilers/libraries, no = do not
 
-AR_CMD='ar cqs'      # Archive command for creating static libraries.
-RM_CMD='/bin/rm -f'  # Command for removing files.
-
 # Flags for large file support
 LFS='-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'
 
@@ -1903,43 +1900,22 @@ fi
 # CUDA
 if [ $USE_CUDA -eq 1 ] ; then
   CUDA_TARGET='cuda_kernels/libcpptraj_cuda.a'
-  cat > src/cuda_kernels/cuda.config.h <<EOF
-AR = $AR_CMD
-DEL_FILE = $RM_CMD
-EOF
-  BuildRules src/cuda_kernels/cuda.config.h nvcc
 fi
 # Readline
 if [ "${LIB_STAT[$LREADLINE]}" = 'bundled' ] ; then
   READLINE_TARGET=${LIB_FLAG[$LREADLINE]}
-  cat > src/readline/readline.config.h <<EOF
-DIRECTIVES = -DHAVE_CONFIG_H
-INCLUDE = -I.
-AR = $AR_CMD
-DEL_FILE = $RM_CMD
-EOF
-  BuildRules src/readline/readline.config.h cc
 else
   READLINE_TARGET='noreadline'
 fi
 # Xdrfile
 if [ "${LIB_STAT[$LXDRFILE]}" = 'bundled' ] ; then
   XDRFILE_TARGET=${LIB_FLAG[$LXDRFILE]}
-  cat > src/xdrfile/xdrfile.config.h <<EOF
-AR = $AR_CMD
-DEL_FILE = $RM_CMD
-EOF
-  BuildRules src/xdrfile/xdrfile.config.h cc
 else
   XDRFILE_TARGET='noxdrfile'
 fi
 # Arpack
 if [ "${LIB_STAT[$LARPACK]}" = 'bundled' ] ; then
   ARPACK_TARGET=${LIB_FLAG[$LARPACK]}
-  cat > src/arpack/arpack.config.h <<EOF
-DEL_FILE = $RM_CMD
-EOF
-  BuildRules src/arpack/arpack.config.h f77
 else
   ARPACK_TARGET='noarpack'
 fi
@@ -1971,8 +1947,6 @@ if [ ! -z "$DBGFLAGS" ] ; then
   echo "DBGFLAGS=$DBGFLAGS" >> config.h
 fi
 cat >> config.h <<EOF
-DEL_FILE = $RM_CMD
-
 SHARED_SUFFIX=$SHARED_SUFFIX
 DIRECTIVES=$DIRECTIVES
 INCLUDE=$INCLUDE
@@ -2002,6 +1976,14 @@ EOF
 #  BuildRules config.h cc cxx
 #fi
 
+# ----- Create config for external libraries -----
+external_config='external.config.h'
+cat > $external_config <<EOF
+# CPPTRAJ config for external libraries.
+# configured using: $CONFIGURECMD
+EOF
+BuildRules $external_config nvcc cc f77
+
 # ----- Create directories if necessary ----------
 if [ ! -e "$CPPTRAJBIN" ] ; then
   mkdir "$CPPTRAJBIN"

doc/cpptraj.lyx

@@ -117,14 +117,14 @@ Cpptraj
  has a wide range of functionality, and makes use of OpenMP/MPI to speed
  up many calculations, including processing ensembles of trajectories and/or
  conducting multiple analyses in parallel with MPI.
-
 \begin_inset CommandInset citation
 LatexCommand citep
 key "Roe2018"
 literal "true"
 
 \end_inset
 
+
 \end_layout
 
 \begin_layout Standard
@@ -13580,7 +13580,7 @@ Mod
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="82" columns="3">
+<lyxtabular version="3" rows="83" columns="3">
 <features islongtable="true" longtabularalignment="center">
 <column alignment="center" valignment="top" width="1.3in">
 <column alignment="center" valignment="top" width="4.5in">
@@ -16021,7 +16021,7 @@ Calculate unit cell volume.
 </cell>
 </row>
 <row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -16030,7 +16030,7 @@ watershell
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -16040,13 +16040,43 @@ Calculate the number of waters in the first and second solvation shells
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
 
 \end_layout
 
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+xtalsymm
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Superimpose symmetry-related parts of a system using crystallographic symmetry
+ operations.
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+X
+\end_layout
+
 \end_inset
 </cell>
 </row>
@@ -31502,6 +31532,134 @@ closest
 As of version 17 this command is CUDA-enabled in CUDA versions of CPPTRAJ.
 \end_layout
 
+\begin_layout Subsection
+xtalsymm
+\end_layout
+
+\begin_layout LyX-Code
+xtalsymm <mask> group <space group> [collect [centroid]]
+\end_layout
+
+\begin_layout LyX-Code
+     	[ first | reference | ref <name> | refindex <#> ]
+\end_layout
+
+\begin_layout LyX-Code
+     	[na <na>] [nb <nb>] [nc <nc>]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+<mask> Select atoms to perform symmetry operations on.
+\end_layout
+
+\begin_layout Description
+group
+\begin_inset space ~
+\end_inset
+
+<space
+\begin_inset space ~
+\end_inset
+
+group> Symmetry space group (e.g.
+
+\begin_inset Quotes eld
+\end_inset
+
+P1
+\begin_inset Quotes erd
+\end_inset
+
+, 
+\begin_inset Quotes eld
+\end_inset
+
+P121
+\begin_inset Quotes erd
+\end_inset
+
+, etc.)
+\end_layout
+
+\begin_layout Description
+[collect] If specified, reimage solvent molecules by atom.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+[centroid] If specified along with collect, reimage solvent molecules by
+ molecule.
+\end_layout
+
+\end_deeper
+\begin_layout Description
+[first
+\begin_inset space ~
+\end_inset
+
+|
+\begin_inset space ~
+\end_inset
+
+reference
+\begin_inset space ~
+\end_inset
+
+|
+\begin_inset space ~
+\end_inset
+
+ref
+\begin_inset space ~
+\end_inset
+
+<name>
+\begin_inset space ~
+\end_inset
+
+|
+\begin_inset space ~
+\end_inset
+
+refindex
+\begin_inset space ~
+\end_inset
+
+<#>] Reference structure to use for determining crystal symmetry.
+\end_layout
+
+\begin_layout Description
+[na
+\begin_inset space ~
+\end_inset
+
+<na>] Number of replicas along the A vector (default 1).
+\end_layout
+
+\begin_layout Description
+[nb
+\begin_inset space ~
+\end_inset
+
+<nb>] Number of replicas along the B vector (default 1).
+\end_layout
+
+\begin_layout Description
+[nc
+\begin_inset space ~
+\end_inset
+
+<nc>] Number of replicas along the C vector (default 1).
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Calculate the optimal approach for superimposing symmetry-related subunits
+ of the simulation back onto one another.
+ This modifies the coordinate state for all future actions.
+\end_layout
+
 \begin_layout Section
 Analysis Commands
 \end_layout

src/Action_ClusterDihedral.cpp

@@ -62,7 +62,7 @@ Action::RetType Action_ClusterDihedral::Init(ArgList& actionArgs, ActionInit& in
 {
 # ifdef MPI
   if (init.TrajComm().Size() > 1) {
-    mprinterr("Error: 'clusterdihedral' not supported with > 1 thread (%i threads currently)\n",
+    mprinterr("Error: 'clusterdihedral' not supported with > 1 process (%i processes currently)\n",
               init.TrajComm().Size());
     return Action::ERR;
   }

src/Action_Contacts.cpp

@@ -54,7 +54,7 @@ Action::RetType Action_Contacts::Init(ArgList& actionArgs, ActionInit& init, int
 # ifdef MPI
   // Since output is to CpptrajFiles, not practical in parallel.
   if (init.TrajComm().Size() > 1) {
-    mprinterr("Error: 'contacts' action does not work with > 1 thread (%i threads currently).\n"
+    mprinterr("Error: 'contacts' action does not work with > 1 process (%i processes currently).\n"
               "Error:   Consider using 'nativecontacts' instead.\n", init.TrajComm().Size());
     return Action::ERR;
   }

src/Action_CreateCrd.cpp

@@ -57,9 +57,9 @@ Action::RetType Action_CreateCrd::Init(ArgList& actionArgs, ActionInit& init, in
     mprintf("\tNot strictly enforcing that all frames have same # atoms.\n");
 # ifdef MPI
   if (init.TrajComm().Size() > 1)
-    mprintf("Warning: Synchronization of COORDS data sets over multiple threads is\n"
+    mprintf("Warning: Synchronization of COORDS data sets over multiple processes is\n"
             "Warning:   experimental and may be slower than reading in via a single\n"
-            "Warning:   thread. Users are encouraged to run benchmarks before\n"
+            "Warning:   process. Users are encouraged to run benchmarks before\n"
             "Warning:   extensive usage.\n");
 # endif
   return Action::OK;

src/Action_CreateReservoir.cpp

@@ -35,7 +35,7 @@ Action::RetType Action_CreateReservoir::Init(ArgList& actionArgs, ActionInit& in
 # endif
 # ifdef MPI
   if (init.TrajComm().Size() > 1) {
-    mprinterr("Error: 'createreservoir' action does not work with > 1 thread (%i threads currently).\n", init.TrajComm().Size());
+    mprinterr("Error: 'createreservoir' action does not work with > 1 process (%i processes currently).\n", init.TrajComm().Size());
     return Action::ERR;
   }
 # endif

src/Action_Density.cpp

@@ -107,8 +107,8 @@ Action::RetType Action_Density::Init(ArgList& actionArgs, ActionInit& init, int
   } else {
 #   ifdef MPI
     if (init.TrajComm().Size() > 1) {
-      mprinterr("Error: 'density' with masks does not work with > 1 thread"
-                " (%i threads currently).\n", init.TrajComm().Size());
+      mprinterr("Error: 'density' with masks does not work with > 1 process"
+                " (%i processes currently).\n", init.TrajComm().Size());
       return Action::ERR;
     }
 # endif

src/Action_FilterByData.cpp

@@ -96,7 +96,7 @@ Action::RetType Action_FilterByData::Init(ArgList& actionArgs, ActionInit& init,
 # ifdef MPI
   if (!multi_ && init.TrajComm().Size() > 1)
     mprintf("Warning: Trajectories written after 'filter' may have issues if\n"
-            "Warning:   the number of threads writing is > 1 (currently %i threads)\n",
+            "Warning:   the number of processes writing is > 1 (currently %i processes)\n",
             init.TrajComm().Size());
 # endif
   return Action::OK;

src/Action_GIST.cpp

@@ -58,7 +58,7 @@ Action::RetType Action_GIST::Init(ArgList& actionArgs, ActionInit& init, int deb
 {
 # ifdef MPI
   if (init.TrajComm().Size() > 1) {
-    mprinterr("Error: 'gist' action does not work with > 1 thread (%i threads currently).\n",
+    mprinterr("Error: 'gist' action does not work with > 1 process (%i processes currently).\n",
               init.TrajComm().Size());
     return Action::ERR;
   }

src/Action_Mask.cpp

@@ -34,7 +34,7 @@ Action::RetType Action_Mask::Init(ArgList& actionArgs, ActionInit& init, int deb
 # ifdef MPI
   trajComm_ = init.TrajComm();
   if ( trajComm_.Size() > 1 && outfile_ != 0) {
-    mprinterr("Error: 'maskout' currently only works with 1 thread (currently %i)\n"
+    mprinterr("Error: 'maskout' currently only works with 1 process (currently %i)\n"
               "Error:   Consider using the 'name'/'out' keywords instead\n", trajComm_.Size());
     return Action::ERR;
   }